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Is the protein folding an aim-oriented process ... - IngentaConnect

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258 M. Brylinski, L. Konieczny <strong>an</strong>d I. Roterm<strong>an</strong>Kyte, J. <strong>an</strong>d Doolittle, R.F. (1982) ‘A simple method for displaying <strong>the</strong> hydropathic characterof a <strong>protein</strong>’, J. Mol. Biol., Vol. 157 pp.105–132.Lamb, M.L., Burdick, K.W., Toba, S., Young, M.M., Skillm<strong>an</strong>, A.G., Zou, X., Arnold, J.R.<strong>an</strong>d Kuntz, I.D. (2001) ‘Design, docking, <strong>an</strong>d evaluation of multiple libraries against multipletargets’, Proteins, Vol. 42, pp.296–318.Levitt, M. (1976) ‘A simplified representation of <strong>protein</strong> conformations for rapid simulation of<strong>protein</strong> <strong>folding</strong>’, J. Mol. Biol., Vol. 104, pp.59–107.Li<strong>an</strong>g, J., Edelsbrunner, H. <strong>an</strong>d Woodward, C. (1998) ‘Anatomy of <strong>protein</strong> pockets <strong>an</strong>d cavities:measurement of binding site geometry <strong>an</strong>d implications for lig<strong>an</strong>d design’, Protein Sci.,Vol. 7, pp.1884–1897.Luque, I. <strong>an</strong>d Freire, E. (2000) ‘Structural stability of binding sites: consequences for bindingaffinity <strong>an</strong>d allosteric effects’, Proteins, Suppl. 4, pp.63–71.Maskos, K., Fern<strong>an</strong>dez-Catal<strong>an</strong>, C., Huber, R., Bourenkov, G.P., Bartunik, H., Ellestad, G.A.,Reddy, P., Wolfson, M.F., Rauch, C.T., Castner, B.J., Davis, R., Clarke, H.R., Petersen, M.,Fitzner, J.N., Cerretti, D.P., March, C.J., Paxton, R.J., Black, R.A. <strong>an</strong>d Bode, W. (1998)‘Crystal structure of <strong>the</strong> catalytic domain of hum<strong>an</strong> tumor necrosis factor-alpha-convertingenzyme’, Proc. Natl. Acad. Sci. USA, Vol. 95, pp.3408–3412.Meiering, E.M., Serr<strong>an</strong>o, L. <strong>an</strong>d Fersht, A.R. (1992) ‘Effect of active site residues in barnase onactivity <strong>an</strong>d stability’, J. Mol. Biol., Vol. 225, pp.585–589.Meirovitch, H. <strong>an</strong>d Scheraga, H.A. (1980a) ‘Empirical studies of hydrophobicity. 2. Distribution of<strong>the</strong> hydrophobic, hydrophilic, neutral, <strong>an</strong>d ambivalent amino acids in <strong>the</strong> interior <strong>an</strong>d exteriorlayers of native <strong>protein</strong>s’, Macromolecules, Vol. 13, pp.1406–1414.Meirovitch, H. <strong>an</strong>d Scheraga, H.A. (1980b) ‘Empirical studies of hydrophobicity. 1. Effectof <strong>protein</strong> size on <strong>the</strong> hydrophobic behavior of amino acids’, Macromolecules, Vol. 13,pp.1398–1405.Meirovitch, H. <strong>an</strong>d Scheraga, H.A. (1981) ‘Empirical studies of hydrophobicity. 3. Radialdistribution of clusters of hydrophobic <strong>an</strong>d hydrophilic amino acids’, Macromolecules,Vol. 14, pp.340–345.Mendez, R., Leplae, R., de Maria, L. <strong>an</strong>d Wodak, S.J. (2003) ‘Assessment of blind predictions of<strong>protein</strong>–<strong>protein</strong> interactions: current status of docking methods’, Proteins, Vol. 52, pp.51–67.Mendez, R., Leplae, R., Lensink, M.F. <strong>an</strong>d Wodak, S.J. (2005) ‘Assessment of CAPRI predictionsin rounds 3-5 shows progress in docking procedures’, Proteins, Vol. 60, pp.150–169.Mom<strong>an</strong>y, F.A., McGuire, R.F., Burgess, A.W. <strong>an</strong>d Scheraga, H.A. (1975) ‘Energy parameters inpolypeptides. VII. Geometric parameters, partial pharges non-bonded interactions, hydrogenbond interactions <strong>an</strong>d intrinsic torsional potentials for naturally occurring amino acids’,J. Phys. Chem., Vol. 79, pp.2361–2381.Nemethy, G., Pottle, M.S. <strong>an</strong>d Scheraga, H.A. (1983) ‘Energy parameters in polypeptides. 9.Updating of geometrical parameters, non-bonding interactions <strong>an</strong>d hydrogen bondinginteractions for naturally occurring amino acids’, J. Phys. Chem., Vol. 87, pp.1883–1887.Nemethy, G., Gibson, K.D., Palmer, K.A., Yoon, C.N., Paterlini, G., Zagari, A., Rumsey, S. <strong>an</strong>dScheraga, H.A. (1992) ‘Energy parameters in polypeptides. 10. Improved geometricalparameters <strong>an</strong>d non-bonded interactions for use in <strong>the</strong> ECEPP/3 algorithm, with application toproline-containing peptides’, J. Phys. Chem., Vol. 96, pp.6472–6484.Novotny, J., Rashin, A.A. <strong>an</strong>d Bruccoleri, R.E. (1988) ‘Criteria that discriminate between native<strong>protein</strong>s <strong>an</strong>d incorrectly folded models’, Proteins, Vol. 4, pp.19–30.Nozaki, Y. <strong>an</strong>d T<strong>an</strong>ford, C. (1970) ‘The solubility of amino acids, diglycine, <strong>an</strong>d triglycine inaqueous gu<strong>an</strong>idine hydrochloride solutions’, J. Biol. Chem., Vol. 245, pp.1648–1652.Ondrechen, M.J., Clifton, J.G. <strong>an</strong>d Ringe D. (2001) ‘THEMATICS: a simple computationalpredictor of enzyme function from structure’, Proc. Natl. Acad. Sci. USA, Vol. 98,pp.12473–12478.Oshiro, C.M., Kuntz, I.D. <strong>an</strong>d Dixon, J.S. (1995) ‘Flexible lig<strong>an</strong>d docking using a geneticalgorithm’, J. Comput. Aided Mol. Des., Vol. 9 pp.113–130.

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